TnSeqCorr

• These are correlations of TnSeq responses across 82 experimental conditions.
• LFCs (log2-fold-changes) were computed for each gene in each condition relative to a relevant control condition (e.g. H37Rv grown on 7H9).
• The LFCs were normalized by dividing by the standard deviation for each condition. (so roughly, |LFC|>2 are the outliers, i.e. tails of the distribution)
• Note that essential genes often have LFCs around 0.
• Data for some genes is not available if they have less than 3 TA sites, or the dynamic range of LFCs is less than 2.0 across all conditions. (This is the case for many essential genes.)
• 'leverage' on each plot is a statistical score that indicates how much the regression is influenced by a few outlier points; the traditional threshold is indicated on the plots (3p/n, which is about 0.07 for this dataset), but in practice, cases with leverage > ~0.2 seem to be the least reliable (most misleading) correlation coefficients.

Top 10 genes with highest correlation to Rv1063c/-:

update plot	correlation	link to info on gene
Rv0004/-	(cc=0.5061)	info on Rv0004/-
Rv2065/cobH	(cc=0.4585)	info on Rv2065/cobH
Rv1795/eccD5	(cc=0.4391)	info on Rv1795/eccD5
Rv2315c/-	(cc=0.4263)	info on Rv2315c/-
Rv1797/eccE5	(cc=0.4231)	info on Rv1797/eccE5
Rv1796/mycP5	(cc=0.4221)	info on Rv1796/mycP5
Rv1783/eccC5	(cc=0.4208)	info on Rv1783/eccC5
Rv3225c/-	(cc=0.4197)	info on Rv3225c/-
Rv2005c/-	(cc=0.408)	info on Rv2005c/-
Rv1782/eccB5	(cc=0.4006)	info on Rv1782/eccB5

Correlation of Rv1063c/- with Rv0004/-

Normalized LFCs for Rv1063c/-:
(description and provenance of datasets)

	Rv1063c/-	Rv0004/-
Fe_supp_jason_reseq	-0.021	0.0
low_pH_jason_reseq	-0.912	0.0
NO_jason_reseq	-0.953	0.0
B6_jason_reseq	-0.292	0.0
MHCII_jason_reseq	0.229	0.0
Isoniazid02	1.12	0.851
Rifampicin4	-0.217	-0.712
Ethambutol3	0.815	0.14
Meropenem3	-0.047	0.266
Vancomycin16	-0.077	-0.698
Rv2680_day32	0.393	0.0
H37Rv_KO_MarP	0.851	-1.865
hypoxia_3wks	-0.494	0.0
hypoxia_6wks	-0.852	0.0
glycerol	-0.082	0.385
cholesterol	0.3	0.0
AJ	-0.269	0.0
Bibs02	0.256	0.0
Bibs02c	0.364	0.0
BL6	-0.493	0.0
BL6a	-0.143	0.0
BXD01	-0.108	0.0
BXD010	-0.486	0.0
BXD011	-0.297	0.0
BXD03	-0.041	0.0
BXD04	-0.487	0.0
BXD05	-0.57	0.0
BXD06	-0.713	0.0
BXD07	-0.716	0.0
BXD08	0.541	0.0
BXD09	-0.31	0.0
CAST	0.155	1.785
CCcont	-0.14	0.0
DS01	0.602	0.0
DS02	0.503	0.0
DS04	-0.246	0.533
DS0c	0.085	0.0
GP01	1.423	2.861
GP02	1.24	1.416
GP0c	1.671	1.663
NOD	2.11	4.852
NZO	-0.392	0.0
PWK	-0.162	0.0
H37Rv_KO_CtpC	-0.281	0.0
H37Rv_KO_CtpD	-0.785	0.127
H37Rv_KO_Rv1272	0.159	0.0
H37Rv_KO_SugABC	0.873	0.55
H37Rv_KO_MbtN	-0.131	0.283
Trans05	0.051	0.0
macrophage_unactivated	0.268	0.0
IL1	-0.439	0.0
Rapamycin	-0.221	0.0
Tcell	0.932	0.0
GMCSF	0.137	0.0
IFNab	0.686	0.0
IFNg	0.273	0.0
IFNg_GMCSF1	0.163	0.826
Rv1432_day32	-0.763	0.0
Rv1565c_day32	0.073	0.0
secA2_input	-0.111	1.526
delta_Rv3594	0.961	0.828
delta_Rv3717	0.24	3.253
delta_Rv3811	0.021	1.387
delta_Rv0954	0.836	-0.178
PonA1	-0.017	-0.159
EccD1_KO	-0.164	0.0
EspI_KO	0.462	0.0
PE35_KO	-0.108	0.368
PPE68_KO	0.0	0.403
glycerol2	-0.251	0.0
lignocerate	-0.089	0.0
oleate	-0.401	0.0
phosphatidylcholine	-0.814	0.0
acetate	-0.199	0.0
glucAc	-0.383	0.0
Rv0950ko	-0.039	-0.793
Rv1096ko	1.046	1.517
Rv3684ko	1.513	1.055
delta_otsA_trehalose	-1.127	0.0